Contents

A computer hacker discovers evidence against the Syndicate that is so damning that its revelation to the public would be nothing short of catastrophic, leading Mulder into a race against sinister agents to learn the truth.

At a Navajo reservation in New Mexico, a teenage boy comes across a boxcar buried in the ground. He retrieves the corpse of an alien-like figure from within it and shows it to his father and grandfather. An older man, Albert Hosteen, has a prophetic moment in which he believes people will come in response to this discovery.

In Dover, Delaware, Kenneth Soona, an associate of the Lone Gunmen, hacks into Department of Defense files and downloads government secrets about aliens onto a digital cassette. Immediately, word of the breach echoes throughout the world, particularly amongst the members of the Syndicate. The Cigarette Smoking Man tells those concerned that he has already resolved the matter. The Lone Gunmen meet with Mulder and tell him that Soona, also known as the Thinker, requests to meet with him. Down the hall, one of Mulder's neighbors shoots her husband, apparently for no reason.

Mulder meets with Soona in the park, who gives him the digital cassette. An excited Mulder returns to FBI headquarters with it, only to find it contains pages of apparent gibberish, which sends him into an irrational rage, calling it someone's idea of a "bad joke." Scully looks closer and thinks she thinks the files are encrypted in Navajo - she remembers her father telling her that it was used as a code during World War II because it was completely indecipherable except to a small group of linguists - even modern Navajos would have trouble with it. While she takes the tape to investigate, Skinner calls Mulder to his office to question him on the tape. Unexpectedly, Mulder attacks him. Scully is later brought before Skinner and other senior FBI officials and is questioned about Mulder's actions. Scully is told that Mulder faces dismissal from the FBI, and she faces a similar sentence if she has lied to them.

On Martha's Vineyard, the Cigarette Smoking Man comes to see Mulder's father and informs him of the theft of the tape, suspecting that Mulder is in possession of it. Scully meets with a Navajo translator, who can only understand some of the words on the tape; she refers Scully to a World War II-era code talker. Mulder is called away to see his father; when Scully arrives at his apartment, she is nearly killed by a bullet fired through his window. Mulder meets with his father, who says he has something important to tell him, but is shot by Krycek when he goes to the bathroom. Mulder's father asks for forgiveness as he passes away in his arms. When Mulder calls Scully, she tells him to flee, and when he arrives at her apartment, she takes his gun while he sleeps.

Scully brings Mulder's gun to the FBI for comparison against the bullet that killed his father. When Mulder awakens, he is upset and suspicious of Scully. That night, returning to his building, Scully finds that Mulder's water is being contaminated. When Mulder arrives home, he finds Krycek there and is about to kill him when Scully shoots Mulder to prevent him from doing so. Krycek escapes.

Scully brings an unconscious Mulder to New Mexico, and when he awakens, she reveals to him that his behavior was caused by a drug placed into his water supply. She introduces him to Albert Hosteen, a Navajo code-talker who has been translating the files on the digital tape. Scully reveals that the tape refers to both her and Duane Barry, as well as some sort of test. Albert introduces Mulder to his grandson, who drives him to where he found the boxcar containing the alien-like corpse. Just before he heads in, he is called by the Cigarette Smoking Man, who is able to trace Mulder's location through the call. Mulder heads inside the boxcar, finding a pile of the dead creatures, each with smallpox vaccination scars on their arms. The Cigarette Smoking Man arrives with armed soldiers and, not finding Mulder inside, orders the boxcar to be burned.

"There was a tribe of Indians who lived here more than 600 years ago. Their name was Anasazi, it means 'ancient aliens'. No evidence of their fate exists. Historians say they disappeared without a trace. They say that because they will not sacrifice themselves to the truth...Nothing disappears without a trace." - Albert Hosteen

This episode's story was inspired by series creator Chris Carter being fascinated with the Anasazi tribe of Native Americans and was further influenced by a vacation he took to Sedona, Arizona. Thus, the Anasazi are not only mentioned in the story but also provide this episode with its name. Carter said of the installment's creation, "This episode was the culmination of a lot of ideas [....] David Duchovny and I worked quite closely on the story and he had a lot of input, and then I sat down and wrote the script." According to Carter, Duchovny was instrumental in coming up with the idea of seemingly killing off one of the series' two lead characters at the end of the episode.

The production team were hard-pressed to find a desert locale in their Vancouver environs, since such a site was required for the New Mexico rock quarry in this episode. The crew ended up filming in an old abandoned quarry that was east of Vancouver, making alterations for the production.

The fistfight between Mulder and Krycek in this episode was choreographed by David Duchovny and Nicholas Lea themselves, as the stunt coordinator had been stuck in traffic. Since Lea was required to repeatedly snap his neck like he was taking a punch, Director R.W. Goodwin ordered a massage therapist to Lea's room the next morning.

Endeavoring to make a specific quarry look as though it was in New Mexico, the production crew painted the quarry with sixteen hundred gallons of red paint. The series' art department painted the scenery to match pictures of Sedona, with rocks of red and orange hues, and painted the entirety of a half-mile of cliff.

Although this episode's story was somewhat initially daunting for the creative staff, Chris Carter ended up being happy with the installment's teleplay. He admitted, "Darin Morgan called this 'the kitchen sink episode' because, it had so much in it, he didn't know how we would pull it off. But I'm very proud of the script." In particular, Carter ultimately thought the presentation of the idea of Mulder apparently dying in the conclusion of this episode, the second season finale, brought a lot of interest to The X-Files and heightened the interest in the series.

Even years after this episode aired, David Duchovny routinely left phone messages for Nicholas Lea that jokingly accused Lea of having murdered Duchovny's father, due to Krycek killing Mulder's father in this episode.